Methylenetetrahydrofolate-dependent biosynthesis of ribothymidine in transfer RNA of Streptococcus faecalis. Evidence for reduction of the 1-carbon unit by FADH2

The methyl carbon of ribothymidine in Loop IV of the tRNA of Streptococcus faecalis, Bacillus subtilis, and some other microorganisms is derived directly from 5,10-methylenetetrahydrofolate, not S-adenosylmethionine. The pure enzyme from S. faecalis also requires FADH2. We have obtained evidence that tetrahydrofolate is a product of the reaction and demonstrated that label from [5-3H]5-deazaFMNH2 is incorporated into the methyl moiety of ribothymidine. These data indicate that the enzyme uses methylenetetrahydrofolate solely as a 1-carbon donor and employs FADH2 as a reducing agent in vitro according to the following reaction: tRNA(U psi C) + CH2 = THF + FADH2 leads to tRNA(T psi C) + THF + FAD.     

Anaerobic protoporphyrin biosynthesis does not require incorporation of methyl groups from methionine.

It was recently reported (H. Akutsu, J.-S. Park, and S. Sano, J. Am. Chem. Soc. 115:12185-12186, 1993) that in the strict anaerobe Desulfovibrio vulgaris methyl groups from exogenous L-methionine are incorporated specifically into the 1 and 3 positions (Fischer numbering system) on the heme groups of cytochrome c3. It was suggested that under anaerobic conditions, protoporphyrin IX biosynthesis proceeds via a novel pathway that does not involve coproporphyrinogen III as a precursor but instead may use precorrin-2 (1,3-dimethyluroporphyrinogen III), a siroheme and vitamin B12 precursor which is known to be derived from uroporphyrinogen III via methyl transfer from S-adenosyl-L-methionine. We have critically tested this hypothesis by examining the production of protoporphyrin IX-based tetrapyrroles in the presence of exogenous [14C]methyl-L-methionine under anaerobic conditions in a strict anaerobe (Chlorobium vibrioforme) and a facultative anaerobe (Rhodobacter capsulatus). In both organisms, 14C was incorporated into the bacteriochlorophyll precursor, Mg-protoporphyrin IX monomethyl ester. However, most of the label was lost upon base hydrolysis of this compound to yield Mg-protoporphyrin IX. These results indicate that although the administered [14C]methyl-L-methionine was taken up, converted into S-adenosyl-L-methionine, and used for methyl transfer reactions, including methylation of the 6-propionate of Mg-protoporphyrin IX, methyl groups were not transferred to the porphyrin nucleus of Mg-protoporphyrin IX. In other experiments, a cysG strain of Salmonella typhimurium, which cannot synthesize precorrin-2 because the gene encoding the enzyme that catalyzes methylation of uroporphyrinogen III at positions 1 and 3 is disrupted, was capable of heme-dependent anaerobic nitrate respiration and growth on the nonfermentable substrate glycerol, indicating that anaerobic biosynthesis of protoporphyrin IX-based hemes does not require the ability to methylate uroporphyrinogen III. Together, these results indicate that incorporation of L-methionine-deprived methyl groups into porphyrins or their precursors is not generally necessary for the anaerobic biosynthesis of protoporphyrin IX-based tetrapyrroles.     

The incorporation of tritiated retinyl moiety into the active-site lysine residue of bacteriorhodopsin.

Purple membranes were isolated from Halobacterium halobium bleached and regenerated with all-trans-[15-3H]retinal. The incorporation of label was 1.2 mol of retinal/mol of bacterio-opsin. The [3H]retinyl-bacterio-opsin obtained from regeneration was hydrolysed to give tritiated retinyl-lysine, which, on hydrogenation to N-epsilon-perhydro[3H]retinyl-lysine and reaction with 1-fluoro-2,4-dinitrobenzene, gave bis-(2,4-dinitrophenyl)-N-epsilon-perhydro[3H]retinyl-lysine. This result confirmed that the retinyl moiety of the chromophore is attached to an epsilon-amino group of lysine.     

Balanced macromolecular biosynthesis in "protoplasts" of Streptococcus faecalis

Osmotically fragile forms of Streptococcus faecalis 9790 were grown in 0.5 m sucrose- or 0.5 m NH(4)Cl-stabilized medium. The "protoplast" cultures exhibit an average growth rate constant of 0.66 to 0.94 mass doublings/hr. In a variety of experiments, turbidity and the net content of protein, ribonucleic acid (RNA) and deoxyribonucleic acid increase at the same rate, indicating balanced macromolecular biosynthesis. A total of two to three mass doublings was obtained, with no evidence of cell division. After osmotic shock, "protoplast" cultures released 93 to 94% of their RNA content in a form not sedimentable at 12,800 x g for 15 min, in contrast to streptococci, which released 7% of their RNA content after the same treatment.     

Serine incorporation into the selenocysteine moiety of glutathione peroxidase

The selenium in mammalian glutathione peroxidase is present as a selenocysteine ([Se]Cys) moiety incorporated into the peptide backbone 41-47 residues from the N-terminal end. To study the origin of the skeleton of the [Se]Cys moiety, we perfused isolated rat liver with 14C- or 3H-labeled amino acids for 4 h, purified the GSH peroxidase, derivatized the [Se]Cys in GSH peroxidase to carboxymethylselenocysteine ([Se]Cys(Cm)), and determined the amino acid specific activity. Perfusion with [14C]cystine resulted in [14C]cystine incorporation into GSH peroxidase without labeling [Se]Cys(Cm), indicating that cysteine is not a direct precursor for [Se]Cys. [14C]Serine perfusion labeled serine, glycine (the serine hydroxymethyltransferase product), and [Se]Cys(Cm) in purified GSH peroxidase, whereas [3-3H]serine perfusion only labeled serine and [Se]Cys(Cm), thus demonstrating that the [Se]Cys in GSH peroxidase is derived from serine. The similar specific activities of serine and [Se]Cys(Cm) strongly suggest that the precursor pool of serine used for [Se] Cys synthesis is the same or similar to the serine pool used for acylation of seryl-tRNAs.     

Tetrahydrofolate-dependent biosynthesis of ribothymidine in transfer ribonucleic acids of Gram-positive bacteria.

Trimethoprim, an inhibitor that prevents tetrahydrofolate-dependent transmethylation reactions inbacteria, was used in a comparative study to discriminate between two possible biosynthetic pathways, either the S-adenosylmethionine or the tetrahydrofolate-dependent formation of ribothymidine (rT) in transfer ribonucleic acids (tRNA's) of several strains of gram-positive and gram-negative microorganisms. rT-deficient tRNA's accumulate in trimethoprim-treated gram-positive Streptococcus faecium, Staphylococcus aureus, Corynebacterium bovis, Arthrobacter albidus, and all examined Bacillaceae, except Bacillus stearothermophilus. The rT-deficient rT-deficient tRNA's accept the methyl moiety from S-adenosylmethionine in vitro, with extracts from Escherichia coli (wild type) as a source of methylating enzymes; 90% of the incorporated methyl groups are present in rT. Trimethoprim does not inhibit the biosynthesis of rT in tRNA of gram-negative Enterobacteriaceae, Rhizobium lupini, and Pseudomonadaceae, suggesting that the rT-specific tRNA methyltransferases of these gram-negative strains use S-adenosylmethionine as coenzyme.     

Studies on the ribothymidine content of specific rat and human tRNAs: a postulated role for 5-methyl cytosine in the regulation of ribothymidine biosynthesis.

Total mammalian tRNAs contain on the average less than one mole of ribothymidine per mole of tRNA. Mammalian tRNAs can be grouped into at least four classes, depending upon their ribothymidine content at position 23 from the 3′ terminus. Class A contains tRNA in which a nucleoside other than uridine replaces ribothymidine (tRNA_i^Met); Class B contains tRNA in which one mole of a modified uridine (rT, ψ, or 2′-O-methylribothymidine) is found per mole of tRNA (tRNA^Ser, tRNA^Trp, and tRNA^Lys, respectively). Class C contains tRNA in which there is a partial conversion of uridine to ribothymidine (tRNA^Phe, tRNA₁^Gly, tRNA₂^Gly); Class D contains tRNA which totally lacks ribothymidine (tRNA^Val). Only those tRNAs in Class C are acceptable substrates for $\text{E.}\text{coli}$ uridine methylase, under the conditions used in these studies. These observations cannot be adequately explained solely on the basis of the presence or absence of a specific “universal” nucleoside other than U or rT at position 23 from the 3′ terminus. However, correlations can be made between the ribothymidine and 5-methylcytosine content of eucaryotic tRNA. We postulate that the presence of one or more 5-methylcytosines in and adjacent to loop III (minor loop) in individual tRNAs act to regulate the amount of ribothymidine formed by uridine methylase. Several experiments are proposed as tests for this hypothesis.     

Transformation of Streptococcus sanguis Challis by plasmid deoxyribonucleic acid from Streptococcus faecalis.

Plasmid deoxyribonucleic acid (DNA) from Streptococcus faecalis, strain DS5, was transferred to the Challis strain of Streptococcus sanguis by transformation. Two antibiotic resistance markers carried by the beta plasmid from strain DS5, erythromycin and lincomycin, were transferred to S. sanguis at a maximum frequency of 1.8 x 10-5/colony-forming unit. Approximately 70% of the covalently closed circular DNA isolated from transformant cultures by dye buoyant density gradients was shown to be hybridizable to beta plasmid DNA. Two major differences were observed between the beta plasmid from S. faecalis and the plasmid isolated from transformed S. sanguis: (i) the beta plasmid from strain DS5 sedimented in velocity gradients at 43S, whereas the covalently closed circular DNA from transformed Challis sedimented at 41S, suggesting a 1.5-Mdal deletion from the beta plasmid occurred; (ii) although the 43S beta plasmid remained in the supercoiled configuration for several weeks after isolation, the 41S plasmid was rapidly converted to a linear double-stranded molecule. Attempts to transform S. sanguis with the alpha plasmid from S. faecalis, strain DS5, were unsuccessful.     

Introduction of the Streptococcus faecalis transposon Tn916 into Bacillus thuringiensis subsp. israelensis

The conjugative Streptococcus faecalis transposon Tn916 was introduced into Bacillus thuringiensis subsp. israelensis by filter matings with S. faecalis. B. thuringiensis transconjugants resistant to tetracycline (Tetr) were detected at a frequency of approximately 7.0 X 10(-7) per recipient cell during filter matings, whereas transfer of Tn916 was not observed in broth matings. The Tetr phenotype in subsp. israelensis was stable in the absence of antibiotic selection. Southern hybridization analysis revealed that Tn916 had inserted into several different sites on the B. thuringiensis subsp. israelensis chromosome but insertion into plasmid DNA was not observed. Movement of Tn916 was demonstrated when Tetr B. thuringiensis transconjugants were mated with isogenic recipients. Southern hybridizations, however, showed that the resulting Tetr isolates contained Tn916 junction fragments that were nearly identical to the donor, suggesting that this movement resulted from transfer of chromosomal DNA from donor to recipient or from a fusion of mating cells, rather than conjugative transposition of the Tn element.     

In vivo and in vitro incorporation of endogenous nucleotides by the energy-transducing ATPase of Streptococcus faecalis

The soluble ATPase isolated from Streptococcus faecalis membranes containing tightly bound endogenous nucleotides do not exchange in the presence of ATP and Mg+2 added during the purification of the enzyme. In this paper the stoichiometry of endogenous nucleotides in the soluble ATPase obtained from (a) growing cells, (b) nongrowing glycolyzing cells, and (c) isolated cell membranes has been defined. The time course of incorporation was also studied in nongrowing, glycolyzing cells and isolated cell membranes. In all cases, 1-2 mol of nucleotide was bound per mol of enzyme. Maximal incorporation required approximately 1 h at 38 degrees C. Incorporation of cytoplasmic nucleotide into the enzyme occurred by a process of slow exchange for bound nucleotide. N,N'-dicyclohexylcarbodiimide, which inhibits the membrane-bound ATPase and prevents generation of the protonmotive force, had no effect on incorporation of endogenous nucleotides in glycolyzing cells. Treatment of glycolyzing cells with gramicidin D plus K+, which dissipates the protonmotive force but has no effect on ATPase activity, did not inhibit incorporation of nucleotide. These results support the view that the slow exchange-incorporation of endogenous nucleotide(s) is independent of ATP hydrolysis and a protonmotive force. An in vitro system for the study of nucleotide binding at endogenous sites is described.     

Biosynthesis of peptidoglycan in Staphylococcus aureus: incorporation of the Nepsilon-Ala-Lys moiety into the peptide subunit of nascent peptidoglycan.

UDP-MurNAc-Ala-DGlu-Lys(Nepsilon-Ala)-DAla-DAla was isolated from extracts of Staphylococcus aureus Copenhagen. This nucleotide accumulated in media deficient in glycine. To establish its role in peptidoglycan biosynthesis, the nucleotide-hexapeptide was compared with UDP-MurNAc-Ala-DGlu-Lys-DAla-DAla in the reaction catalyzed by phospho-MurNAc-pentapeptide translocase and in the membrane-catalyzed nascent peptidoglycan-synthetizing system. In the exchange reaction catalyzed by the translocase, the Rmax and Rmax/Km are 1.79 muM/min and 4.47 X 10(-2)/min, respectively, for UDP-MurNAc-pentapeptide and 1.81 muM/min and 4.46 X 10(-2)/min, respectively, for UDP-Mur-NAc-hexapeptide. In the synthesis of nascent peptidoglycan, the Vmax is 1.8 muM/min X 10(-2) for both the nucleotide-hexapeptide and -pentapeptide. The Vmax/Km is 5.6 X 10(-4) and 4.3 X 10(-4)/min for the nucleotide-pentapeptide and -hexapeptide, respectively. Schleifer, Hammes, and Kandler (Adv. Microb. Physiol. in press) observed that growth of S. aureus Copenhagen on a glycine-poor medium results in a peptidoglycan structure in which 20% of the lysine residues are substituted at the epsilon-amino group by L-alanine residues that do not participate in interpeptide bridge information. The in vitro studies demonstrate that UDP-MurNAc-Ala-DGlu-Lys(Nepsilon-Ala)-DAla-DAla is a possible precursor of the Nepsilon-Ala-Lys moiety.     

Immobilization and treatment of Streptococcus faecalis for the continuous conversion of arginine into citrulline.

Citrulline is one of the steps of the arginine dihydrolase system of Streptococcus faecalis. We have shown that the bacteria, immobilized in polyacrylamide gel and treated with Cetyl trimethyl ammonium bromide (CTAB) or heat, were able to convert arginine to citrulline. Used continuously in a column reactor, the entrapped cells have a stable enzymatic activity for at least 30 days at 45 degrees C.